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Default behavior is unchanged (-svx --pdb on all tests). Pass args to override, e.g. ./tests/pytest_in_docker.sh -sv tests/test_status.py Also supports running from a git worktree by mounting the main .git dir. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Split bidsapp_run.sh.jinja2 into a run-only script and a standalone zip_outputs.sh.jinja2. Bootstrap generates <name>_run.sh always and <name>_zip.sh only when zip_foldernames is present in the config. participant_job.sh now issues two separate datalad run calls when zipping: one for the container (-o outputs/) and one for zipping (-o *.zip). Without zip_foldernames, only the container run executes. Also update check_setup to expect _run.sh instead of _zip.sh. Tests: unit tests for no-zip run script, zip script, and submit script generation (both with and without zip). E2e test with a no-zip config verifies loose output files in the output RIA after merge. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Makes zipping optional. As implemented though, it will cause issues with babs status has_results calculation, which relies on the existence of zips.
Once babs status refactor merges, I think we rebase this one, and we can make the changes to how
has_resultsgets calculated as a part of this PR